Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.998251320707924 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:184550501A>GN/A show variant in all transcripts   IGV
HGNC symbol VPS8
Ensembl transcript ID ENST00000424463
Genbank transcript ID N/A
UniProt peptide Q8N3P4
alteration type single base exchange
alteration region CDS
DNA changes c.247A>G
cDNA.336A>G
g.20571A>G
AA changes I83V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 83
frameshift no
known variant Reference ID: rs9830734
databasehomozygous (G/G)heterozygousallele carriers
1000G81511441959
ExAC95291370923238
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3571
0.6341
(flanking)4.3571
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased20578wt: 0.9078 / mu: 0.9515 (marginal change - not scored)wt: AGATGAGTCTTTTATTCTTGAGGATCCTACATTGTTAAACA
mu: AGATGAGTCTTTTGTTCTTGAGGATCCTACATTGTTAAACA		 ttga|GGAT
Acc marginally increased20576wt: 0.2731 / mu: 0.2838 (marginal change - not scored)wt: GAAGATGAGTCTTTTATTCTTGAGGATCCTACATTGTTAAA
mu: GAAGATGAGTCTTTTGTTCTTGAGGATCCTACATTGTTAAA		 tctt|GAGG
Acc marginally increased20580wt: 0.7669 / mu: 0.7957 (marginal change - not scored)wt: ATGAGTCTTTTATTCTTGAGGATCCTACATTGTTAAACATT
mu: ATGAGTCTTTTGTTCTTGAGGATCCTACATTGTTAAACATT		 gagg|ATCC
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      83LNETDDEDESFILEDPTLLNIDTI
mutated  all conserved    83LNETDDEDESFVLEDPTLLNIDT
Ptroglodytes  no homologue    
Mmulatta  all conserved  ENSMMUG00000000425  83LNETDDEDESFVLEDPTLLNIDT
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000033653  83LNETDDEDESFVLEDPTLLNVDT
Ggallus  no alignment  ENSGALG00000006704  n/a
Trubripes  all conserved  ENSTRUG00000003896  32LNELEDEEEPFVLEDTCVLNTDN
Drerio  all identical  ENSDARG00000060477  56LNEPEDEDEPFILEDTCLLNTEN
Dmelanogaster  not conserved  FBgn0035704  68LSEFEADSDVASEFGMPV------
Celegans  all conserved  C42C1.4  39LNDTENLSDPFLDEQFAVDGEFGSVSNLTE
Xtropicalis  no alignment  ENSXETG00000018613  n/a
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 495 / 495
position (AA) of stopcodon in wt / mu AA sequence 165 / 165
position of stopcodon in wt / mu cDNA 584 / 584
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 90 / 90
chromosome 3
strand 1
last intron/exon boundary 537
theoretical NMD boundary in CDS 397
length of CDS 495
coding sequence (CDS) position 247
cDNA position
(for ins/del: last normal base / first normal base)		 336
gDNA position
(for ins/del: last normal base / first normal base)		 20571
chromosomal position
(for ins/del: last normal base / first normal base)		 184550501
original gDNA sequence snippet ATGATGAAGATGAGTCTTTTATTCTTGAGGATCCTACATTG
altered gDNA sequence snippet ATGATGAAGATGAGTCTTTTGTTCTTGAGGATCCTACATTG
original cDNA sequence snippet ATGATGAAGATGAGTCTTTTATTCTTGAGGATCCTACATTG
altered cDNA sequence snippet ATGATGAAGATGAGTCTTTTGTTCTTGAGGATCCTACATTG
wildtype AA sequence MENEPDHENV EQSLCAKTSE EELNKSFNLE ASLSKFSYID MDKELEFKND LIDDKEFDIP
QVDTPPTLES ILNETDDEDE SFILEDPTLL NIDTIDSHSY DTSSVASSDS GDRTNLKRKK
KLPDSFSLHG SVMRHSLLKG ISAQIVSAAD KVDAGLPTAI VSIL*
mutated AA sequence MENEPDHENV EQSLCAKTSE EELNKSFNLE ASLSKFSYID MDKELEFKND LIDDKEFDIP
QVDTPPTLES ILNETDDEDE SFVLEDPTLL NIDTIDSHSY DTSSVASSDS GDRTNLKRKK
KLPDSFSLHG SVMRHSLLKG ISAQIVSAAD KVDAGLPTAI VSIL*
speed 0.94 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project